back from Lyon

More cathedral than train station?

I’m just back from a short trip to Lyon, attending the kick-off meeting of our new EU research project, EvoEvo (“Evolution of Evolution”), selected for the FET Proactive “Evolving Living Technologies” call.  It was an excellent meeting, promising lots of interesting and exciting research over the next three years.  Our task at York is to develop a novel bio-inspired algorithm for tackling open-ended problems, based on the biological experiments and computational modelling being done by the other partners.  It’s going to be great fun.

It was my first trip to Lyon.  A 90 minute EasyJet flight from Stansted arrived at Terminal 3 in Lyon Saint-Exupéry airport, which is a sort of temporary high tech cowshed with metal walls and a plastic roof.

blue sky!

Sights architectural improved rapidly at the adjacent railway station, with its gorgeous swooping roof.  From there is was a 30 minute shuttle-tram ride into Lyon itself, then a shorter tram ride to the hotel.

… amoeba-table

amoeba basin …

The hotel itself, although perfectly comfortable and fine, had clearly embraced some form of crazed design concept. The first clue there was something different about the place was its stealth lifts, entrances cunningly camouflaged with a garish mural.  Then there was the the shape and colour of the hand basin in the en suite, manifesting as some sort of fluorescent green amoeboid entity.  This was clearly deliberate, as its colour and shape were mirrored by the small table in the room proper.

I never actually
tried sitting on this

looks like steel;
feels like lino

The decor continued in a sort of industrial-chic flavour, with a tin chair, and faux riveted brushed steel flooring (actually a very pleasant-feeling warm lino).

This being France, the food was, of course, excellent.  Even a mere sandwich from an airport cafe on the return trip was delicious.  On the Monday we sat outside to eat lunch in glorious sunshine.  It was blustery (probably the edge of St Jude’s storm), but very warm: I was actually rather concerned about the possibility of sunburn!

Another short hop, back to Stansted.  The flight arrived 10 minutes ahead of schedule, due to a strong tail wind (yet more remnants of the storm).  By happy chance I ended up first in the queue at passport control, and was thinking about where I had to go to get the bus to the airport carpark.  I realised the guy looking at my passport had asked me a question. Uhh. Rewind.  Oh, he’d said: “where was your flight from today?”  I looked at him blankly.  I’m in Stansted.  That means I’ve just flown in from somewhere.  Where?  Taormina?  No.  Where then?  Uhh...  Oh.  “Lyon”, I said, after a long, suspicious pause.  He looked more closely at my passport, but then let me through.  Whew.

So, safely back home.  Now to get down to the research…

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snail central

We have a few piles of old tiles in the garden, waiting to be repurposed.  These snails clearly think that the gap between two piles is a home from home.

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sequestering carbon, several books at a time XI

Two weeks’ worth:

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90 minutes later

If you don't like the weather, wait 15 minutes.

Ah, that's better!  Lovely sunshine, warm breezes.  So, we now have a couple of bags full of apples, ready to take to work and inflict on our colleagues on Monday.

The sunshine is making the berries look gorgeous.

Cotoneaster berries shining in the sunlight

a contrast in colours: yellow berries of the berberis against purple heuchera leaves

Notice the mushrooms nestling in the bottom left of that picture?  Well, the whole crop has been growing well in the damp:

I just wish I knew if they were safe to eat.  I am very firmly assuming not.

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apple picking time

Prediction is very difficult, especially about the future. — Niels Bohr (attrib.)

Our apple glut is reaching fruition, so it’s time to start harvesting.  Shall we pick them today, or tomorrow?  Let’s have a look at the BBC weather forecast.  It says today will be dry up until this evening, then rain continuing for most of tomorrow.  Great, let’s harvest today, then.

Off out into the garden, picking apples.  We’d been out, ooh, must have been all of five minutes, when … you’ve guessed it, it started to rain!

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PythonTeX

I write technical documents in LaTeX, and my programming language of choice is (currently) Python.  I’m about to start writing a large LaTeX document that will have lots of figures drawn with Python’s matplotlib.  So, I was wondering, wouldn’t it be nice if there was some support for including these more directly in the document.  I went surfing, and came across PythonTeX, by Geoffrey M. Poore.

PythonTeX doesn’t just allow you to put figures in your LaTeX, it allows whole chunks of Python, with the results embedded in the output.  After watching a YouTube video on the capabilities, I thought it looked interesting, so I decide to give it a go: it might well be useful, and anyway it’s a great displacement activity from actually starting writing that document.

It wasn’t a particularly onerous installation process, as LaTeX and Python installations go.  In order to get the test document, pythontex_gallery.tex, to format properly, I just had to:

1. download PythonTeX
2. run LaTeX on the provided example file pythontex_gallery.tex (I use TeXnicCenter)
3. give LaTeX permission install several macro packages (as warned by the PythonTeX installation documentation)
4. from the command line, run pythontex.py pythontex_gallery.tex
5. scrutinise the error messages to see I needed pygments.style, sympy, and scipy  (again, as warned by the PythonTeX installation documentation)
6. go to the pygments page, and see that it recommends installation via ez_setup
7. go to the ez_setup page, and download it
8. from the command line, run python ez_setup.py
9. download the relevant pygments “egg”
10. from the command line, run easy_install Pygments-1.6-py2.7.egg
11. download and install sympy
12. download and install scipy (hence discovering that it is pronounced “sigh pie”, not “skippy”)
13. from the command line, run pythontex.py pythontex_gallery.tex
14. run LaTeX on pythontex_gallery.tex again

At this point out popped a LaTeX pdf with figures, equations, integrals, and expression derivations all produced from the embedded python!

Now that I have everything installed, all I have to do to generate this pdf from scratch is:

1. run LaTeX on pythontex_gallery.tex
2. from the command line, run pythontex.py pythontex_gallery.tex
3. run LaTeX on pythontex_gallery.tex again

Simples!

There is also a handy utility to convert the LaTeX file with embedded python into a stand-alone LaTeX document, suitable for other people to process.  (This is essential if the document needs to be sent off for publication, for example.)

1. edit the LaTeX file to include the depythontex=true option in the pythontex package
2. run LaTeX on pythontex_gallery.tex again
3. run pythontex.py pythontex_gallery.tex again
4. run depythontex.py --graphicspath pythontex_gallery.tex final.tex

Then anyone can run LaTeX on final.tex without needing PythonTeX.

Having installed PythonTeX, and checked that it can at least process the supplied test file, I next needed to check that I can get it to produce the kind of diagrams I want.

So I wrote a short LaTeX document with the body:

\begin{pylabcode}
n = 16
m = 6
figure(figsize=(n*0.2, m*0.2))
gca().axison = False
x = 8
y = 4
fill( (x,x+1,x+1,x), (y,y,y+1,y+1), 'r', linewidth=0)
for i in range(0,n+1):
    ii = (i,i)
    jj = (0,m)
    plot(ii,jj,'0.4', linewidth=0.2)
for j in range(0,m+1):
    ii = (0,n)
    jj = (j,j)
    plot(ii,jj,'0.4', linewidth=0.2)
savefig('myplot.pdf', bbox_inches='tight')
\end{pylabcode}

\includegraphics{myplot.pdf}

This is a \pylab{'${0} \\times {1} = {2}$'.format(n, m, n * m)}
square grid, with a red block at $(\pylab{x},\pylab{y})$.

The top bit is some python code to draw a grid and a red square, and the bottom bit is some explanatory LaTeX text.  Going through the LaTeX-PythonTex-LaTeX process gives:

Excellent.  I can use it to draw diagrams in situ.  The great advantage this approach has is that I can keep all my code for the figures in the same file as the LaTeX text, so there will be much less chance for fragments to wander off and get lost.

As shown in the code above, the LaTeX can include references to python variables, which is how the caption part is generated.  Then, if I decide that I want a slightly different figure, I just edit this single file, change only the values assigned to n,m,x,y in the python part, and get something like:

The new variable values have changed the drawn figure, and these changes have also been propagated to the caption, including the calculation of the product.  This gives a much more sophisticated form of cross referencing.

I’m sold!

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too much tech!

So, there I was, sitting at my computer, waiting for a Google hangout to start (an excellent way to have a meeting, btw – video on one screen, Google doc on another, everyone typing up the notes in the doc – works really well, at least for smallish groups).

My computer’s webcam is throwing a wobbly at the moment, so I had my tablet ready to run the hangout itself.  The hangout organiser sent the invitation.  My computer notified me.  My tablet’s screen lit up, notifying me.  What I hadn’t been expecting was that my phone, sitting next to my tablet, would also suddenly come alive, notifying me!

I’m surrounded by tech, all demanding to talk to me…

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mushrooms gonna mushroom

We've had mushrooms in the garden before, but going out today, the sight was just surreal.

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sequestering carbon, several books at a time X

Three weeks’ worth of input, partly populated as a result of me reading Mattessich’s 1982 survey of Systems Theory literature (“The Systems Approach: Its Variety of Aspects”), because the author “decided to concentrate mainly on books” in that survey.  Naturally, several of the concentrate appear in this pile.  Some others appear because they were brought to my attention on blogs that I read.

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Martin Magnus on Kindle

There are books that we’ve seen, usually read, and want to own, but can’t find available (or sometimes, affordable!) copies.  Then the hunt is on, scouring the second hand lists, lurking, waiting, and, if we are lucky, pouncing.

We each had a classic example of this from our childhood.  Charles was after Martin Magnus on Mars, the third in the series, only ever published in hardback, and tough to find.  So tough that, before the advent of the web, Charles was seriously wondering if he’d just imagined it! However, he eventually spotted a copy for sale, and pounced.

I had a similar story with Annabel and Bryony, a delightful children’s book I read when much younger.  I did at least know it existed, since my sister had a copy.  Eventually, after much hunting, I got my own copy, a present from my sister who had spotted it lurking in a second hand bookshop in Robin Hood's Bay.  And later still, thanks to my review of it on the web, I got a further trilogy.

This evening, Charles announced: “Such a long challenge, rendered insignificant.  Martin Magnus on Mars is on Kindle!”  And so it is.  At least we paid only a couple of quid for the hardback.  And there is something different about a physical copy.

Wait, I thought.  If MMoM is on Kindle, what about A&B?  Sure enough, it too can now be had in non-dead tree format.

The times they are a-changin’.  But I wouldn’t part with my hardback copy, battered dust jacket and all.

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a sky full of shepherd's delight

Great sunset tonight.

Interestingly, this isn’t looking towards the setting sun, but about 90° west of it.

A different part of the sky:

This view is diametrically opposite the setting sun.

No photo of the setting sun itself – in that direction there’s just thick black cloud!

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mellow fruitfulness

Our apple tree, in the early morning sunlight.

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